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Sun C, Schuman E. A multi-omics view of neuronal subcellular protein synthesis. Curr Opin Neurobiol 2023; 80:102705. [PMID: 36913750 DOI: 10.1016/j.conb.2023.102705] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 03/13/2023]
Abstract
While it has long been known that protein synthesis is necessary for long-term memory in the brain, the logistics of neuronal protein synthesis is complicated by the extensive subcellular compartmentalization of the neuron. Local protein synthesis solves many of the logistic problems posed by the extreme complexity of dendritic and axonal arbors and the huge number of synapses. Here we review recent multi-omic and quantitative studies that elaborate a systems view of decentralized neuronal protein synthesis. We highlight recent insights from the transcriptomic, translatomic, and proteomic levels, discuss the nuanced logic of local protein synthesis for different protein features, and list the missing information needed to build a comprehensive logistic model for neuronal protein supply.
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Affiliation(s)
- Chao Sun
- Max Planck Institute for Brain Research, Frankfurt, Germany; Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Denmark; Aarhus University, Department of Molecular Biology and Genetics, Universitetsbyen 81, 8000 Aarhus C, Denmark. https://twitter.com/LukeChaoSun
| | - Erin Schuman
- Max Planck Institute for Brain Research, Frankfurt, Germany.
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2
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Jin LQ, Zhou Y, Li YS, Zhang G, Hu J, Selzer ME. Transcriptomes of Injured Lamprey Axon Tips: Single-Cell RNA-Seq Suggests Differential Involvement of MAPK Signaling Pathways in Axon Retraction and Regeneration after Spinal Cord Injury. Cells 2022; 11:cells11152320. [PMID: 35954164 PMCID: PMC9367414 DOI: 10.3390/cells11152320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 02/01/2023] Open
Abstract
Axotomy in the CNS activates retrograde signals that can trigger regeneration or cell death. Whether these outcomes use different injury signals is not known. Local protein synthesis in axon tips plays an important role in axon retraction and regeneration. Microarray and RNA-seq studies on cultured mammalian embryonic or early postnatal peripheral neurons showed that axon growth cones contain hundreds to thousands of mRNAs. In the lamprey, identified reticulospinal neurons vary in the probability that their axons will regenerate after axotomy. The bad regenerators undergo early severe axon retraction and very delayed apoptosis. We micro-aspirated axoplasms from 10 growing, 9 static and 5 retracting axon tips of spinal cord transected lampreys and performed single-cell RNA-seq, analyzing the results bioinformatically. Genes were identified that were upregulated selectively in growing (n = 38), static (20) or retracting tips (18). Among them, map3k2, csnk1e and gtf2h were expressed in growing tips, mapk8(1) was expressed in static tips and prkcq was expressed in retracting tips. Venn diagrams revealed more than 40 components of MAPK signaling pathways, including jnk and p38 isoforms, which were differentially distributed in growing, static and/or retracting tips. Real-time q-PCR and immunohistochemistry verified the colocalization of map3k2 and csnk1e in growing axon tips. Thus, differentially regulated MAPK and circadian rhythm signaling pathways may be involved in activating either programs for axon regeneration or axon retraction and apoptosis.
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Affiliation(s)
- Li-Qing Jin
- Shriners Hospitals Pediatric Research Center, The Lewis Katz School of Medicine (LKSOM) at Temple University, Philadelphia, PA 19140, USA; (G.Z.); (J.H.)
- Department of Neural Sciences, Lewis Katz School of Medicine (LKSOM), 3500 North Broad Street, Philadelphia, PA 19140, USA
- Correspondence: (L.-Q.J.); (M.E.S.)
| | - Yan Zhou
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, PA 19111, USA;
| | - Yue-Sheng Li
- DNA Sequence & Genomics Core Facility at the NHLBI, Bethesda, MD 20892, USA;
| | - Guixin Zhang
- Shriners Hospitals Pediatric Research Center, The Lewis Katz School of Medicine (LKSOM) at Temple University, Philadelphia, PA 19140, USA; (G.Z.); (J.H.)
- Department of Neural Sciences, Lewis Katz School of Medicine (LKSOM), 3500 North Broad Street, Philadelphia, PA 19140, USA
| | - Jianli Hu
- Shriners Hospitals Pediatric Research Center, The Lewis Katz School of Medicine (LKSOM) at Temple University, Philadelphia, PA 19140, USA; (G.Z.); (J.H.)
- Department of Neural Sciences, Lewis Katz School of Medicine (LKSOM), 3500 North Broad Street, Philadelphia, PA 19140, USA
| | - Michael E. Selzer
- Shriners Hospitals Pediatric Research Center, The Lewis Katz School of Medicine (LKSOM) at Temple University, Philadelphia, PA 19140, USA; (G.Z.); (J.H.)
- Department of Neural Sciences, Lewis Katz School of Medicine (LKSOM), 3500 North Broad Street, Philadelphia, PA 19140, USA
- Department of Neurology, Lewis Katz School of Medicine (LKSOM), 3500 North Broad Street, Philadelphia, PA 19140, USA
- Correspondence: (L.-Q.J.); (M.E.S.)
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3
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Sahoo PK, Willis DE, Sleigh JN. Editorial: Pathways and Processes Underpinning Axonal Biology and Pathobiology. Front Mol Neurosci 2022; 15:883244. [PMID: 35401108 PMCID: PMC8984018 DOI: 10.3389/fnmol.2022.883244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/02/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Pabitra K. Sahoo
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Dianna E. Willis
- Burke Neurological Institute, White Plains, NY, United States
- Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, New York, NY, United States
| | - James N. Sleigh
- Department of Neuromuscular Diseases and UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
- UK Dementia Research Institute, University College London, London, United Kingdom
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4
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Eastman G, Sharlow ER, Lazo JS, Bloom GS, Sotelo-Silveira JR. Transcriptome and Translatome Regulation of Pathogenesis in Alzheimer's Disease Model Mice. J Alzheimers Dis 2022; 86:365-386. [PMID: 35034904 DOI: 10.3233/jad-215357] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Defining cellular mechanisms that drive Alzheimer's disease (AD) pathogenesis and progression will be aided by studies defining how gene expression patterns change during pre-symptomatic AD and ensuing periods of declining cognition. Previous studies have emphasized changes in transcriptome, but not translatome regulation, leaving the ultimate results of gene expression alterations relatively unexplored in the context of AD. OBJECTIVE To identify genes whose expression might be regulated at the transcriptome and translatome levels in AD, we analyzed gene expression in cerebral cortex of two AD model mouse strains, CVN (APPSwDI;NOS2 -/- ) and Tg2576 (APPSw), and their companion wild type (WT) strains at 6 months of age by tandem RNA-Seq and Ribo-Seq (ribosome profiling). METHODS Identical starting pools of bulk RNA were used for RNA-Seq and Ribo-Seq. Differential gene expression analysis was performed at the transcriptome, translatome, and translational efficiency levels. Regulated genes were functionally evaluated by gene ontology tools. RESULTS Compared to WT mice, AD model mice had similar levels of transcriptome regulation, but differences in translatome regulation. A microglial signature associated with early stages of Aβ accumulation was upregulated at both levels in CVN mice. Although the two mice strains did not share many regulated genes, they showed common regulated pathways related to AβPP metabolism associated with neurotoxicity and neuroprotection. CONCLUSION This work represents the first genome-wide study of brain translatome regulation in animal models of AD and provides evidence of a tight and early translatome regulation of gene expression controlling the balance between neuroprotective and neurodegenerative processes in brain.
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Affiliation(s)
- Guillermo Eastman
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay.,Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Elizabeth R Sharlow
- Department of Pharmacology, University of Virginia, Charlottesville, VA, USA
| | - John S Lazo
- Department of Pharmacology, University of Virginia, Charlottesville, VA, USA.,Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - George S Bloom
- Department of Biology, University of Virginia, Charlottesville, VA, USA.,Department of Cell Biology, University of Virginia, Charlottesville, VA, USA.,Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
| | - José R Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay.,Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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5
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Mesquita-Ribeiro R, Fort RS, Rathbone A, Farias J, Lucci C, James V, Sotelo-Silveira J, Duhagon MA, Dajas-Bailador F. Distinct small non-coding RNA landscape in the axons and released extracellular vesicles of developing primary cortical neurons and the axoplasm of adult nerves. RNA Biol 2021; 18:832-855. [PMID: 34882524 PMCID: PMC8782166 DOI: 10.1080/15476286.2021.2000792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Neurons have highlighted the needs for decentralized gene expression and specific RNA function in somato-dendritic and axonal compartments, as well as in intercellular communication via extracellular vesicles (EVs). Despite advances in miRNA biology, the identity and regulatory capacity of other small non-coding RNAs (sncRNAs) in neuronal models and local subdomains has been largely unexplored.We identified a highly complex and differentially localized content of sncRNAs in axons and EVs during early neuronal development of cortical primary neurons and in adult axons in vivo. This content goes far beyond miRNAs and includes most known sncRNAs and precisely processed fragments from tRNAs, sno/snRNAs, Y RNAs and vtRNAs. Although miRNAs are the major sncRNA biotype in whole-cell samples, their relative abundance is significantly decreased in axons and neuronal EVs, where specific tRNA fragments (tRFs and tRHs/tiRNAs) mainly derived from tRNAs Gly-GCC, Val-CAC and Val-AAC predominate. Notably, although 5'-tRHs compose the great majority of tRNA-derived fragments observed in vitro, a shift to 3'-tRNAs is observed in mature axons in vivo.The existence of these complex sncRNA populations that are specific to distinct neuronal subdomains and selectively incorporated into EVs, equip neurons with key molecular tools for spatiotemporal functional control and cell-to-cell communication.
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Affiliation(s)
| | - Rafael Sebastián Fort
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Alex Rathbone
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Joaquina Farias
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.,Polo de Desarrollo Universitario "Espacio de Biología Vegetal del Noreste", Centro Universitario Regional Noreste, UdelaR, Uruguay
| | - Cristiano Lucci
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Victoria James
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Jose Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Maria Ana Duhagon
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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6
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Di Paolo A, Garat J, Eastman G, Farias J, Dajas-Bailador F, Smircich P, Sotelo-Silveira JR. Functional Genomics of Axons and Synapses to Understand Neurodegenerative Diseases. Front Cell Neurosci 2021; 15:686722. [PMID: 34248504 PMCID: PMC8267896 DOI: 10.3389/fncel.2021.686722] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/02/2021] [Indexed: 01/02/2023] Open
Abstract
Functional genomics studies through transcriptomics, translatomics and proteomics have become increasingly important tools to understand the molecular basis of biological systems in the last decade. In most cases, when these approaches are applied to the nervous system, they are centered in cell bodies or somatodendritic compartments, as these are easier to isolate and, at least in vitro, contain most of the mRNA and proteins present in all neuronal compartments. However, key functional processes and many neuronal disorders are initiated by changes occurring far away from cell bodies, particularly in axons (axopathologies) and synapses (synaptopathies). Both neuronal compartments contain specific RNAs and proteins, which are known to vary depending on their anatomical distribution, developmental stage and function, and thus form the complex network of molecular pathways required for neuron connectivity. Modifications in these components due to metabolic, environmental, and/or genetic issues could trigger or exacerbate a neuronal disease. For this reason, detailed profiling and functional understanding of the precise changes in these compartments may thus yield new insights into the still intractable molecular basis of most neuronal disorders. In the case of synaptic dysfunctions or synaptopathies, they contribute to dozens of diseases in the human brain including neurodevelopmental (i.e., autism, Down syndrome, and epilepsy) as well as neurodegenerative disorders (i.e., Alzheimer's and Parkinson's diseases). Histological, biochemical, cellular, and general molecular biology techniques have been key in understanding these pathologies. Now, the growing number of omics approaches can add significant extra information at a high and wide resolution level and, used effectively, can lead to novel and insightful interpretations of the biological processes at play. This review describes current approaches that use transcriptomics, translatomics and proteomic related methods to analyze the axon and presynaptic elements, focusing on the relationship that axon and synapses have with neurodegenerative diseases.
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Affiliation(s)
- Andres Di Paolo
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Departamento de Proteínas y Ácidos Nucleicos, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Joaquin Garat
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Guillermo Eastman
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Joaquina Farias
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Polo de Desarrollo Universitario “Espacio de Biología Vegetal del Noreste”, Centro Universitario Regional Noreste, Universidad de la República (UdelaR), Tacuarembó, Uruguay
| | - Federico Dajas-Bailador
- School of Life Sciences, Medical School Building, University of Nottingham, Nottingham, United Kingdom
| | - Pablo Smircich
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - José Roberto Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
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7
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Di Paolo A, Farias J, Garat J, Macklin A, Ignatchenko V, Kislinger T, Sotelo Silveira J. Rat Sciatic Nerve Axoplasm Proteome Is Enriched with Ribosomal Proteins during Regeneration Processes. J Proteome Res 2021; 20:2506-2520. [PMID: 33793244 DOI: 10.1021/acs.jproteome.0c00980] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Axons are complex subcellular compartments that are extremely long in relation to cell bodies, especially in peripheral nerves. Many processes are required and regulated during axon injury, including anterograde and retrograde transport, glia-to-axon macromolecular transfer, and local axonal protein synthesis. Many in vitro omics approaches have been used to gain insight into these processes, but few have been applied in vivo. Here we adapted the osmotic ex vivo axoplasm isolation method and analyzed the adult rat sciatic-nerve-extruded axoplasm by label-free quantitative proteomics before and after injury. 2087 proteins groups were detected in the axoplasm, revealing translation machinery and microtubule-associated proteins as the most overrepresented biological processes. Ribosomal proteins (73) were detected in the uninjured axoplasm and increased their levels after injury but not within whole sciatic nerves. Meta-analysis showed that detected ribosomal proteins were present in in vitro axonal proteomes. Because local protein synthesis is important for protein localization, we were interested in detecting the most abundant newly synthesized axonal proteins in vivo. With an MS/MS-BONCAT approach, we detected 42 newly synthesized protein groups. Overall, our work indicates that proteomics profiling is useful for local axonal interrogation and suggests that ribosomal proteins may play an important role, especially during injury.
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Affiliation(s)
- Andres Di Paolo
- Departamento de Proteínas y Ácidos Nucleicos, IIBCE, 11600 Montevideo, Uruguay.,Departamento de Genómica, IIBCE, 11600 Montevideo, Uruguay
| | | | - Joaquin Garat
- Departamento de Genómica, IIBCE, 11600 Montevideo, Uruguay
| | - Andrew Macklin
- Princess Margaret Cancer Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Vladimir Ignatchenko
- Princess Margaret Cancer Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - José Sotelo Silveira
- Departamento de Genómica, IIBCE, 11600 Montevideo, Uruguay.,Departamento de Biología Celular y Molecular, Facultad de Ciencias, 11400 Montevideo, Uruguay
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8
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Waldron A, Yajima M. Localized translation on the mitotic apparatus: A history and perspective. Dev Biol 2020; 468:55-58. [PMID: 32979335 DOI: 10.1016/j.ydbio.2020.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/10/2020] [Accepted: 09/16/2020] [Indexed: 10/23/2022]
Abstract
Localized translation is a proposed biological event that allows mRNA to be translated on site, providing an additional level of protein regulation within a cell. Examples of localized translation have been found or proposed in a variety of cellular contexts from neurons to cancer cells and implicated in both normal development and disease for over a half century. For example, mRNA translation on the mitotic apparatus (MA) was initially hypothesized in the 1950-60s. However, its proof of existence, biological significance and mechanistic details have remained sparse and it is still unclear how well conserved this mechanism may be among different cell types or organisms. In this review, we provide a brief historic summary of translation on the MA and discuss how current and future work may help us understand this biological process that provides a subcellular level of regulation in protein synthesis within a cell.
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Affiliation(s)
- Ashley Waldron
- Department of Molecular Biology Cell Biology Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI 02912, USA
| | - Mamiko Yajima
- Department of Molecular Biology Cell Biology Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI 02912, USA.
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9
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Farias J, Holt CE, Sotelo JR, Sotelo-Silveira JR. Axon microdissection and transcriptome profiling reveals the in vivo RNA content of fully differentiated myelinated motor axons. RNA (NEW YORK, N.Y.) 2020; 26:595-612. [PMID: 32051223 PMCID: PMC7161357 DOI: 10.1261/rna.073700.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/31/2020] [Indexed: 05/23/2023]
Abstract
Axonal protein synthesis has been shown to play a role in developmental and regenerative growth, as well as in the maintenance of the axoplasm in a steady state. Recent studies have begun to identify the mRNAs localized in axons, which could be translated locally under different conditions. Despite that by now hundreds or thousands of mRNAs have been shown to be localized into the axonal compartment of cultured neurons in vitro, knowledge of which mRNAs are localized in mature myelinated axons is quite limited. With the purpose of characterizing the transcriptome of mature myelinated motor axons of peripheral nervous systems, we modified the axon microdissection method devised by Koenig, enabling the isolation of the axoplasm RNA to perform RNA-seq analysis. The transcriptome analysis indicates that the number of RNAs detected in mature axons is lower in comparison with in vitro data, depleted of glial markers, and enriched in neuronal markers. The mature myelinated axons are enriched for mRNAs related to cytoskeleton, translation, and oxidative phosphorylation. Moreover, it was possible to define core genes present in axons when comparing our data with transcriptomic data of axons grown in different conditions. This work provides evidence that axon microdissection is a valuable method to obtain genome-wide data from mature and myelinated axons of the peripheral nervous system, and could be especially useful for the study of axonal involvement in neurodegenerative pathologies of motor neurons such as amyotrophic lateral sclerosis (ALS) and spinal muscular atrophies (SMA).
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Affiliation(s)
- Joaquina Farias
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, 11600, Uruguay
- Departamento de Proteínas y Ácidos Nucléicos, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, 11600, Uruguay
| | - Christine E Holt
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, United Kingdom
| | - José R Sotelo
- Departamento de Proteínas y Ácidos Nucléicos, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, 11600, Uruguay
| | - José R Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, 11600, Uruguay
- Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, 11400, Uruguay
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